NAME

UNAFold.pl — fold an RNA or DNA sequence with lots of output

SYNOPSIS

UNAFold.pl [OPTION]... FILE [FILE]

DESCRIPTION

If one FILE is specified, UNAFold.pl folds the (first) sequence in FILE with hybrid-ss-min, and then computes the h-num and ss-count values. If two FILEs are specified, UNAFold.pl hybridized the first sequence in each FILE with hybrid-min. All output files are named with a prefix which consists of the file name(s) with the extension .seq removed. The loop free energy decomposition is written to prefix.det or prefix.det.html. If boxplot_ng is available, the enrgy dot plot is created in Postscript format and, if possible, in PNG, JPEG or GIF format. Likewise, if sir_graph_ng or sir_graph is available, each structure is drawn in Postscript and, if possible, PNG/JPEG/GIF formats. In addition, each structure is available in XRNA ss format, and the complete set of foldings in RNAML format is written to prefix.rnaml. Finally, in HTML mode, prefix.html contains links to all of the output.

OPTIONS

-n, --NA=RNA2|RNA3|RNA|DNA: set nucleic acid type to RNA or DNA. Default is RNA.
-t, --temp=REAL: set folding temperature to REAL °C. Default is 37.
-N, --sodium=REAL: set Sodium ion concentration to REAL molar. Default is 1.
-M, --magnesium=REAL: set Magnesium ion concentration to REAL molar. Default is 0.
-p, --polymer: use salt corrections for polymers instead of oligomers (the default).
-I, --noisolate: prohibit all isolated basepairs. Isolated basepairs are helices of length 1; that is, they do not stack on another basepair on either side. (See also the --prefilter option below.)
-m, --maxbp=NUMBER: bases farther apart than NUMBER cannot form. Default is no limit.
-c, --constraints=FILE: read a list of constraints from FILE. Constraints must be in the form "P i j k" or "F i j k". These are equivalent to specifying "--prohibit=i,j,k" and "--force=i,j,k", respectively. If FILE is not specified, it defaults to prefix.aux.
-C, --circular: treat sequences as circular rather than linear.
--intra: perform hybridization with intramolecular basepairs.
-P, --percent=REAL: set the energy increment to REAL percent. Defauls is 5.
-W, --window=NUMBER: set the window parameter to NUMBER. Default is determined by sequence length.
-X, --max=NUMBER: set the maximum number of foldings to NUMBER. Default is 100.
--ann=none|p-num|ss-count: optionally produce plots annotated with p-num or ss-count values. Default is none.
--mode=auto|bases|lines: produce structures drawn with bases or lines. Default is auto.
--label=NUMBER: label every NUMBERth base.
--rotate=REAL: rotate structures by REAL degrees.
--run-type=text|html: produce output in plain text (the default) or HTML.
--model=EM|PF: perform an energy minimization (the default) or partition function calculation. In partition function mode, stochastic tracebacks replace the mfold sample and a probability dot plot replaces the energy dot plot.
--circular: treat sequence as circular rather than linear.
--intra: hybridize sequences allowing intramolecular basepairs.

OBSCURE OPTIONS

--allpairs: allow basepairs to form between any two nucleotides. When --allpairs is not specified, only Watson-Crick and wobble basepairs are allowed.
--maxloop=NUMBER: set the maximum size of bulge/interior loops to NUMBER. Default is 30.
--maxas=NUMBER: set the maximum asymmetry of bulge/interior loops to NUMBER. Default is 30.
--nodangle: remove single-base stacking from consideration.
--simple: makes the penalty for multibranch loops constant rather than affine.
--prefilter=value1[,value2]: set the prefilter to filter out all basepairs except those in groups of value2 adjacent basepairs of which value1 can form. value2 is the same as value1 if unspecified. Default is 2 of 2. (See also the --noisolate option above.)

ENVIRONMENT

UNAFOLDDAT: an alternate location from which to read the energy rules. The default energy rules can be overridden with files in the current directory or in the directory pointed to by UNAFOLDDAT. UNAFold.pl looks for each file first in the current directory, then in the directory specified by UNAFOLDDAT and last in /usr/local/share/unafold (or wherever the energy rules were installed).

REFERENCES

Markham, N. R. and Zuker, M. (2008) UNAFold: software for nucleic acid folding and hybridization. In Keith, J. M., editor, Bioinformatics, Volume II. Structure, Functions and Applications, number 453 in Methods in Molecular Biology, chapter 1, pages 3-31. Humana Press, Totowa, NJ. ISBN 978-1-60327-428-9.

Other references which may be useful may be found at http://www.unafold.org/Dinamelt/dinamelt-references.php

AUTHORS

Nick Markham <markham@alum.rpi.edu> and Michael Zuker <zukerm@alum.mit.edu>

COPYRIGHT

AVAILABILITY

UNAFold is available from http://www.unafold.org/Dinamelt/software/obtaining-unafold.php. Commercial use requires a license; see https://ipo.rpi.edu/invention/unafold-version-40.